SEARCH · PubMed Health

Results for “recognition code”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

PubMed2000

Structure of nicotinamide mononucleotide adenylyltransferase: a key enzyme in NAD(+) biosynthesis.

BACKGROUND: Nicotinamide adenine dinucleotide (NAD(+)) is an essential cofactor involved in fundamental processes in cell metabolism. The enzyme nicotinamide mononucleotide adenylyltransferase (NMN AT) plays a key role in NAD(+) biosynthesis, catalysing the condensation of nicotinamide mononucleotide and ATP, and yielding NAD(+) and pyrophosphate. Given its vital role in cell life, the enzyme represents a possible target for the development of new antibacterial agents. RESULTS: The structure of NMN AT from Methanococcus jannaschii in complex with ATP has been solved by X-ray crystallography at 2.0 A resolution, using a combination of single isomorphous replacement and density modification techniques. The structure reveals a hexamer with 32 point group symmetry composed of alpha/beta topology subunits. The catalytic site is located in a deep cleft on the surface of each subunit, where one ATP molecule and one Mg(2+) are observed. A strictly conserved HXGH motif (in single-letter amino acid code) is involved in ATP binding and recognition. CONCLUSIONS: The structure of NMN AT closely resembles that of phosphopantetheine adenylyltransferase. Remarkably, in spite of the fact that the two enzymes share the same fold and hexameric assembly, a striking difference in their quaternary structure is observed. Moreover, on the basis of structural similarity including the HXGH motif, we identify NMN AT as a novel member of the newly proposed superfamily of nucleotidyltransferase alpha/beta phosphodiesterases. Our structural data suggest that the catalytic mechanism does not rely on the direct involvement of any protein residues and is likely to be carried out through optimal positioning of substrates and transition-state stabilisation, as is proposed for other members of the nucleotidyltransferase alpha/beta phosphodiesterase superfamily.

Adenosine Triphosphate↗

PubMed1999

Molecular characterization of Escherichia coli FtsE and FtsX.

The genes ftsE and ftsX are organized in one operon together with ftsY. FtsY codes for the receptor of the signal recognition particle (SRP) that functions in targeting a subset of inner membrane proteins. We have found no indications for a structural relationship between FtsE/X and FtsY. Evidence is presented that FtsE and FtsX form a complex in the inner membrane that bears the characteristics of an ATP-binding cassette (ABC)-type transporter. FtsE is a hydrophilic nucleotide-binding protein that has a tendency to dimerize and associates with the inner membrane through an interaction with the integral membrane protein FtsX. An FtsE null mutant showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport.

ATP-Binding Cassette Transporters↗

PubMed1977

Cytotoxic T-cell response to Ectromelia virus-infected cells. Different H-2 requirements for triggering precursor T-cell induction or lysis by effector T cells defined by the BALB/c-H-2db mutation.

The T(c)-cell response to ectromelia virus infection was studied in BALB/c-H-2(db) mice which carry a loss mutation in the H-2D region that results in the absence from cell surfaces of a molecule (D') bearing certain public H-2 specificities. When infected, these mice showed a poor response of T(c) cells that recognize H-2D(d) plus virus-specific determinants on infected macrophage targets, but gave a normal response to H-2K d plus virus-specific antigens. However, their own infected macrophages do display wild-type antigenic patterns involving virus and H-2D(d) since they were killed as efficiently as wild-type (BALB/c,H- 2(d))-infected cells by T(c) cells specific only for H-2D(d) plus viral antigens. When tested in vitro, infected BALB/c-H-2(db) cells stimulated a poor T(c)-cell response to H-2D plus virus-specific antigens, but stimulated a normal response (in comparison with infected BALB/c macrophages) to H-2K(d) plus viral antigens. Uninfected BALB/c-H-2(db) cells stimulated a normal T(c)-cell response to minor H antigens or trinitrophenyl in association with H-2D(d), thus suggesting that the defective response to infection may reside in a failure of the relevant H-2D(d) antigens of mutant cells to physically associate with viral antigens. Close association of viral and H-2D-coded molecules was also suggested by ability of specific anti-H-2K or -H-2D to partially block T(c)-cell-mediated lysis of infected targets. These results were interpreted to mean that H-2Dd-dependent, virus- immune T(c) cells recognized an antigenic pattern consisting of virus- specific and H-2D(d) determinants with the latter borne on an H-2D molecule carrying serologically-defined H-2D(d) private specificities. A second H-2D(d)-coded molecule (D') was not required for recognition and lysis by activated T(c) cells, but was apparently necessary for efficient stimulation of precursor T(c) cells, perhaps by promoting appropriate physical association of viral and H-2D(d) molecules.

Animals↗

PubMed2001

The non-coding RNAs as riboregulators.

The non-coding RNAs database (http://biobases.ibch.poznan.pl/ncRNA/) contains currently available data on RNAs, which do not have long open reading frames and act as riboregulators. Non-coding RNAs are involved in the specific recognition of cellular nucleic acid targets through complementary base pairing to control cell growth and differentiation. Some of them are connected with several well known developmental and neuro-behavioral disorders. We have divided them into four groups. This paper is a short introduction to the database and presents its latest, updated edition.

Animals↗

PubMed1996

The Injury Severity Score is unable to differentiate between poor care and severe injury.

UNLABELLED: The Injury Severity Score (ISS) has been the most frequently used tool for stratifying injured patients. The primary hypothesis of this study was that ISS fails to differentiate between severe injury and mismanagement. METHODS: Data models were generated for mismanaged and ideally managed patients for isolated injuries for each body system. Flow charts of care, outcomes, and Abbreviated Injury Scale (AIS) and ISS scores were generated for each model. RESULTS: Multiple models demonstrated that minor injuries that were mismanaged would result in AIS and ISS scores that were the same as ideally managed severe injuries. Three examples are summarized as follows: A comparison of two patients with splenic injuries demonstrates that ISS is unable to differentiate between mismanagement of a minor splenic laceration as compared to a severely lacerated spleen. In the case of the minor injury to the spleen (initial AIS = 2) that was missed by the treating physicians and allowed to bleed into shock and near arrest because of massive hemorrhage that could have been prevented by early recognition and treatment, the final AIS is coded as 4 in this mismanaged patient, the same AIS and ISS as a severely lacerated spleen (AIS = 4) managed well. Both result in a discharge ISS of 16. Similarly, the ISS at discharge is the same for a well-managed severe head injury (AIS = 4) and a mismanaged minor head injury that is unrecognized, progresses and leads to coma (AIS = 4). Finally AIS, ISS does not differentiate between a well-managed cervical fracture with complete cord injury and a mismanaged cervical spine fracture that initially does not involve a cord injury, but because of mismanagement and lack of immobilization, progresses to complete cord injury because of poor care. Both result in the same injury severity assessment (AIS = 5, ISS = 25 in both). CONCLUSIONS: This study demonstrates a fact that should be recognized by all who rely upon the ISS for comparing quality of care: ISS fails to differentiate severe injury from mismanagement of injury. Because the ISS mixes outcome data with injury severity, ISS incorrectly assigns increased severity to the lesser injuries of mismanaged patients. These findings have important implications for use of the ISS in quality of care assessments.

Abbreviated Injury Scale↗

PubMed1987

Blocking of delivery of the antigen-mediated signal to the nucleus of T cells by cyclosporine.

Cyclosporine (CsA) inhibits release of interleukin 2 (IL-2) and hemopoietic growth activities such as interleukin 3 (IL-3) from major histocompatibility complex (MHC)-antigen-activated T cells. Production of both lymphokines appears to be coordinately regulated; the antigen dose response, T cell dose response, and time course of lymphokine appearance are similar. The triggering of lymphokine production by these cells is solely dependent on T cell-target cell interaction, as the T cell dose response curve indicates that no cooperation occurs between T cells, and any metabolic contribution by the target cell was eliminated by ultraviolet irradiation. This interaction triggers the transcription of lymphokine-encoding mRNA. The process of lymphokine release can be divided into 4 steps: Antigen binds to the T cell; a signal is transferred to the cell nucleus; transcription of lymphokine-encoding mRNA occurs; and intact lymphokine is synthesized and secreted. CsA inhibits antigen triggered lymphokine production. However, it does not inhibit lymphokine release from the constitutively producing tumor cell lines WEHI-3 (which releases IL-3) and MLA 144 (which produces IL-2). Thus CsA has no effects on the lymphokine secretion process or any direct action upon lymphokine-coding mRNA. CsA does not affect antigen recognition during cell-mediated cytotoxicity. Therefore, CsA acts after antigen binding and before transcription of lymphokine-encoding mRNA. That is CsA blocks the transmission of the antigen signal. This information is used to show that this CsA-sensitive signal is required continuously to maintain the T cell in a lymphokine-secreting state.

Animals↗

PubMed1987

Cytotoxic T cell specificity for respiratory syncytial virus proteins: fusion protein is an important target antigen.

We examined the specificity of BALB/c cytotoxic T (Tc) cells for respiratory syncytial virus (RSV) components, using recombinant vaccinia viruses (VV) coding for several individual RSV proteins. We found that immunization with the different VVs yielded the following Tc memory cell populations: high levels of RSV-specific Tc cells were induced with the fusion protein VV, but low levels were induced with VV coding for the RSV nucleoprotein. Tc cell recognition of attachment glycoprotein, part of the matrix molecule or 1A internal protein was poor. While high levels of fusion protein-specific Tc cells were induced by the fusion protein VV, they showed poor cross-reactivity between the A2 and 8/60 RSV strains compared with Tc cells primed by RSV infection.

Animals↗

PubMed2001

SGP-1: prediction and validation of homologous genes based on sequence alignments.

Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of depends little on species-specific properties such as codon usage or the nucleotide distribution. may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors.

Algorithms↗

PubMed1995

Temporal coding of amplitude and frequency modulation in the rat auditory cortex.

The rat primary auditory cortex was explored for neuronal responses to pure tones and sinusoidally amplitude-modulated (SAM) and frequency-modulated (SFM) stimuli. Units showed phase-locked responses to SAM stimulation (55%) and SFM stimulation (80%), with modulation frequencies up to 18 Hz. Tuning characteristics to the modulation frequency were mainly band-pass with best modulation frequencies (BMFs) between 4 and 15 Hz. Units with synchronized activity to SFM stimulation showed three response types with respect to the direction of the frequency modulation: 52% were selective to the upward direction, 30% to the downward direction, and 18% had no preference. Triangular frequency modulations were used to test if units were tuned to specific modulation frequencies or to specific rates of frequency change. In the vast majority of units tested the response characteristics were strongly influenced by varying the modulation frequency, whereas varying the rate of frequency change had little effect in the stimulus range used. Units that showed phase-locked responses to SAM and SFM stimulation had similar activity patterns in response to both types of stimuli. BMFs for SAM and SFM stimulation were significantly correlated. Intrinsic oscillations of up to 20 Hz could be seen in the spontaneous activity and after the stimuli independent of the stimulus type. Oscillation frequencies were significantly correlated with the BMFs of the respective units. The results are discussed in terms of a mechanism for periodicity detection based on a temporal code. This could be important for the recognition of complex acoustic signals.

Acoustic Stimulation↗

PubMed1993

Stationary phase-specific expression of the fic gene in Escherichia coli K-12 is controlled by the rpoS gene product (sigma 38).

The fic gene, near pabA located at 75 min of the Escherichia coli chromosome, was previously identified as the regulatory factor of cell division. In this paper we have examined how fic gene expression is controlled during the growth cycle using a fic-lacZ protein fusion plasmid (pFL1). Its expression was induced at stationary phase while it was nearly abolished in rpoSmutants. Using a RNase protection assay, fic transcript at stationary phase was detected in rpoS+ strains, but not in the rpoS mutants. Furthermore, primer extension analysis indicated that the fic transcript controlled by RpoS initiates at a G located 185 bp upstream from ATG of the fic coding region. Compared with the sigma 70 recognition sequence, the -10 region of fic promoter resembled the Pribnow box, but no homologous sequence was observed at the -35 region. These results were consistent with the characteristic sequence profile of fic promoter recognized specifically by RpoS in vitro, which is the only example of the type III promoter so far detected in vitro and in vivo.

Bacterial Proteins↗

PubMed1999

Effect of gene conversion on polymorphic patterns at major histocompatibility complex loci.

The pattern of polymorphisms at MHC loci was studied by computer simulations and by DNA sequence analyses, with special reference to synonymous and non-synonymous divergence among alleles. A model of overdominance plus short-term selection was simulated for a gene family with allelic and non-allelic gene conversion. It was found that the ratio of non-synonymous-to-synonymous divergence among alleles decreases as the non-allelic conversion becomes more frequent. On the other hand, the ratio of synonymous divergence at the antigen recognition site to that at non-coding region increases by non-allelic conversion. By comparing such a pattern with the observed values of mammalian genes, it is suggested that non-allelic conversion is less frequent in human genes than in genes of other mammals. A quantitative analysis on the patchwork pattern was attempted by using identity excess among nucleotide sites of a gene. Comparison of simulation results with DNA data analysis shows that the rate of allelic conversion is high.

Animals↗

PubMed1988

Inhibition of self-binding antibodies (autobodies) by a VH-derived peptide.

The self-binding properties of a dominant idiotypic antibody (T15) and a minor idiotypic antibody (M603), both specific for phosphorylcholine, were examined as models of self-binding antibodies (autobodies). Observed differences in the self-binding affinity of T15 and M603 relate to variable sequence differences in their respective heavy and light chains. A molecular recognition theory based on the translation of coding and noncoding DNA strands was used to identify complementary amino acid sequences responsible for self-binding. The second hypervariable region of the heavy chain domain, extending into the third framework region, was predicted as the primary self-binding locus. Among peptides synthesized with different variable heavy and light chain regions, a 24-residue peptide spanning the second hypervariable and third framework regions of the heavy chain of T15 was nearly as effective as phosphorycholine in inhibiting the self-binding complexes.

Amino Acid Sequence↗

PubMed1990

Evidence that modulation requires sequences downstream of the promoters of two vir-repressed genes of Bordetella pertussis.

Gene expression in Bordetella pertussis is altered by environmental signals in a process called antigenic modulation. In the presence of modulating signals, expression of several known virulence factors and outer membrane proteins is coordinately reduced. From a bank of TnphoA fusions, we have identified five genes whose expression profiles are reciprocal of those of the major virulence determinants; that is, alkaline phosphatase activity is maximal during growth in the presence of the modulators nicotinic acid and MgSO4 (S. Knapp and J. J. Mekalanos, J. Bacteriol. 170:5059-5066, 1988). We have called these loci vir-repressed genes (vrg). Two of these gene fusions (vrg-6 and vrg-18) have been cloned in Escherichia coli, returned on low-copy-number plasmids to several strains of B. pertussis, and found to be regulated similarly to the fusions harbored on the chromosome. Deletions of the two vrg promoters were constructed and returned to B. pertussis. Regulation was maintained even when all but 24 nucleotides upstream of the vrg-18 initiation codon and 60 nucleotides upstream of the vrg-6 initiation codon were deleted, suggesting that cis-acting regulatory elements of these genes lie very near or within the coding region. We observed a 21-base palindromic sequence overlapping an 8-base direct repeat within the signal sequence coding region of vrg-6; insertion of a 6-bp linker in this region abolished regulation. These repetitive sequences are also at the site of greatest primary sequence identify between vrg-6 and vrg-18 and correspond to the signal sequence coding region. We propose models that involve recognition of this region by a vir-regulated gene product.

Alkaline Phosphatase↗

PubMed2002

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

BACKGROUND: Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. RESULTS: The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined. CONCLUSIONS: We have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.

5' Flanking Region↗

PubMed2006

CARD15/NOD2 mutations in Crohn's disease.

Inflammatory bowel diseases (IBDs) are complex genetic disorders characterized by a complex interplay between genetic and environmental risk factors. At least ten genes or anonymous loci have been proposed to play a role in IBD. Among them, the best studied is CARD15/NOD2, a gene coding for a protein involved in bacterial recognition by cells involved in innate immunity. Despite a large amount of work, a consensus model explaining the effect of Card 15/NoD2 mutations did not emerge, and the disease mechanisms are still subject to debate.

Chromosome Mapping↗

PubMed2005

Distributed neural plasticity for shape learning in the human visual cortex.

Expertise in recognizing objects in cluttered scenes is a critical skill for our interactions in complex environments and is thought to develop with learning. However, the neural implementation of object learning across stages of visual analysis in the human brain remains largely unknown. Using combined psychophysics and functional magnetic resonance imaging (fMRI), we show a link between shape-specific learning in cluttered scenes and distributed neuronal plasticity in the human visual cortex. We report stronger fMRI responses for trained than untrained shapes across early and higher visual areas when observers learned to detect low-salience shapes in noisy backgrounds. However, training with high-salience pop-out targets resulted in lower fMRI responses for trained than untrained shapes in higher occipitotemporal areas. These findings suggest that learning of camouflaged shapes is mediated by increasing neural sensitivity across visual areas to bolster target segmentation and feature integration. In contrast, learning of prominent pop-out shapes is mediated by associations at higher occipitotemporal areas that support sparser coding of the critical features for target recognition. We propose that the human brain learns novel objects in complex scenes by reorganizing shape processing across visual areas, while taking advantage of natural image correlations that determine the distinctiveness of target shapes.

Form Perception↗

PubMed1992

Phoneme recognition by deaf individuals using the multichannel nucleus cochlear implant.

Experiments have been carried out to determine which cues are used in phoneme identification by deaf individuals using a cochlear implant. Five deaf individuals with a Nucleus 22-channel cochlear implant were tested with open set speech audiometry in free field without lipreading. Speech material consisted of lists of Dutch words of the Consonant-Vowel-Consonant type (CVC-words). Word scores ranged from 0 to 22%, phoneme scores from 11 to 54%. For each subject the responses to the initial consonant, the vowel and the final consonant were entered into separate confusion matrices. Kruskal analysis, which provided a geometric representation of these confusions, showed that in the recognition of consonants the feature of voicing is all important. Vowels were identified on the basis of the frequencies of the first and second formants. In one subject the electrode array could only partially be inserted into the cochlea, leaving roughly half the second formant area of the electrode array outside the cochlea. For this subject vowel identification was based upon the first formant and vowel duration; there was no contribution of second formant information to vowel identification. Compressing the first and second formant frequency to the limited intracochlear array did not enhance transmission of second formant information and did not improve performance. The basic findings for consonant and vowel recognition could be explained by the speech coding strategy of the Nucleus speech processor in which voicing determines stimulus periodicity and formant frequencies determine channel selection. Kruskal analysis of phoneme confusions may aid in programming and evaluating the performance of the Nucleus cochlear implant.

Adult↗

PubMed2000

Effect of stimulation rate on cochlear implant recipients' thresholds and maximum acceptable loudness levels.

Clinically, speech processor programs are created using electrical thresholds and maximum acceptable loudness levels (MALs) at several different stimulation rates to determine what rate will provide cochlear implant recipients with the best speech recognition when using fast-rate speech coding strategies. This study was designed to determine the difference in thresholds and MALs (expressed in the clinical unit, Current Level [CL]) for pairs of six rates spanning those available with the Nucleus 24 device (i.e., 250 to 2,400 pps/ch) using monopolar, 25 microsec/phase stimulation. Test-retest measures of threshold and MAL for each rate were obtained from seven adult Nucleus 24 recipients on each of 11 electrodes. The difference in threshold and in MAL between pairs of rates was dependent on the absolute CL. Below approximately 190 CL, thresholds and MALs decreased with increasing rate; above 210 CL, there was little change in threshold or MAL with increasing rate. Based on these findings, an approach to estimating threshold and MAL from one rate to another is suggested, pending further research.

Adult↗